packages feed

GrammarProducts 0.1.0.0 → 0.1.1.0

raw patch · 6 files changed

+59/−61 lines, 6 filesdep ~ADPfusiondep ~FormalGrammarsdep ~PrimitiveArrayPVP ok

version bump matches the API change (PVP)

Dependency ranges changed: ADPfusion, FormalGrammars, PrimitiveArray

API changes (from Hackage documentation)

Files

FormalLanguage/GrammarProduct/Op/Add.hs view
@@ -1,7 +1,7 @@  module FormalLanguage.GrammarProduct.Op.Add where -import Control.Lens hiding (outside)+import Control.Lens hiding (outside,indices) import Control.Lens.Fold import Control.Newtype import Data.List (genericReplicate)@@ -43,10 +43,11 @@                                 (l^.rules <> r^.rules) --                                  s                                 (l^.params <> r^.params)+                                (l^.indices <> r^.indices)                                 (l^.grammarName <> r^.grammarName)                                 False     where s | l^.start == r^.start = l^.start-            | l^.start /= mempty && r^.start /= mempty = error "add new start symbol"+            | l^.start /= mempty && r^.start /= mempty = l^.start -- error "add new start symbol" -- TODO to be discussed ?!             | l^.start == mempty                       = r^.start             |                       r^.start == mempty = l^.start
FormalLanguage/GrammarProduct/Op/Linear.hs view
@@ -9,7 +9,7 @@  import Control.Arrow ((&&&)) import Data.Semigroup-import Control.Lens hiding (outside)+import Control.Lens hiding (outside,indices) import Control.Applicative import qualified Data.Set as S import Data.List (groupBy,nub)@@ -30,14 +30,15 @@   instance Semigroup (Linear Grammar) where-  (Linear g) <> (Linear h) = Linear $ Grammar sv st tv io rs s p (g^.grammarName ++ h^.grammarName) False where -- ts ns es rs s (g^.name <> h^.name) where-    sv = M.fromList . nub . map (_name &&& id) . concatMap _getSymbolList . uniqueSyntacticSymbols $ set rules rs def -- build a temporary @def@ grammar, extract symbols from that one-    st = g^.synterms <> h^.synterms-    tv = g^.termvars <> h^.termvars-    io = g^.outside-    rs = S.fromList [ direct l r | l <- g^..rules.folded, r <- h^..rules.folded ]-    s  = (g^.start) <> (h^.start)-    p  = (g^.params) <> (h^.params)+  (Linear g) <> (Linear h) = Linear $ Grammar sv st tv io rs s p ixs (g^.grammarName ++ h^.grammarName) False where -- ts ns es rs s (g^.name <> h^.name) where+    sv  = M.fromList . nub . map (_name &&& id) . concatMap _getSymbolList . uniqueSyntacticSymbols $ set rules rs def -- build a temporary @def@ grammar, extract symbols from that one+    st  = g^.synterms <> h^.synterms+    tv  = g^.termvars <> h^.termvars+    io  = g^.outside+    rs  = S.fromList [ direct l r | l <- g^..rules.folded, r <- h^..rules.folded ]+    s   = (g^.start) <> (h^.start)+    p   = (g^.params) <> (h^.params)+    ixs = (g^.indices) <> (h^.indices)     direct l r = Rule (l^.lhs <> r^.lhs) (l^.attr <> r^.attr) (mergeRHS (l^.rhs) (r^.rhs))     {-     ts = g^.tsyms <> h^.tsyms
FormalLanguage/GrammarProduct/Op/Subtract.hs view
@@ -3,7 +3,7 @@  import           Control.Arrow ((&&&)) import           Control.Lens.Fold-import           Control.Lens hiding (outside)+import           Control.Lens hiding (outside,indices) import           Control.Newtype import           Data.List (genericReplicate) import           Data.Semigroup@@ -24,14 +24,15 @@     | dim l /= dim r           = error $ printf "grammars %s and %s have different dimensions, cannot unify. (subtract)" (show l) (show r)     | l^.outside /= r^.outside = error $ printf "grammars %s and %s have different inside/outside annotation." (show l) (show r)     | otherwise                = g-    where sv = M.fromList . map ((_name &&& id) . fst) . uniqueSynVarsWithTape       $ g-          st = M.fromList . map ((_name &&& id) . fst) . uniqueSynTermsWithTape      $ g-          tv = M.fromList . map ((_name &&& id) . fst) . uniqueBindableTermsWithTape $ g-          io = l^.outside-          rs = (l^.rules) S.\\ (r^.rules)-          s  = if (anyOf (folded . lhs) ((l^.start) ==) rs) then l^.start else Symbol []-          p  = M.union (l^.params) (r^.params)-          g  = Grammar sv st tv io rs s p (l^.grammarName ++ r^.grammarName) False+    where sv  = M.fromList . map ((_name &&& id) . fst) . uniqueSynVarsWithTape       $ g+          st  = M.fromList . map ((_name &&& id) . fst) . uniqueSynTermsWithTape      $ g+          tv  = M.fromList . map ((_name &&& id) . fst) . uniqueBindableTermsWithTape $ g+          io  = l^.outside+          rs  = (l^.rules) S.\\ (r^.rules)+          s   = if (anyOf (folded . lhs) ((l^.start) ==) rs) then l^.start else Symbol []+          p   = M.union (l^.params) (r^.params)+          ixs = M.union (l^.indices) (r^.indices)+          g   = Grammar sv st tv io rs s p ixs (l^.grammarName ++ r^.grammarName) False  {- subtract l r
GrammarProducts.cabal view
@@ -1,8 +1,9 @@ name:           GrammarProducts-version:        0.1.0.0+version:        0.1.1.0 author:         Christian Hoener zu Siederdissen, 2013-2015 copyright:      Christian Hoener zu Siederdissen, 2013-2015-homepage:       http://www.bioinf.uni-leipzig.de/gADP/+homepage:       https://github.com/choener/GrammarProducts+bug-reports:    https://github.com/choener/GrammarProducts/issues maintainer:     choener@bioinf.uni-leipzig.de category:       Formal Languages, Bioinformatics license:        GPL-3@@ -13,6 +14,8 @@ tested-with:    GHC == 7.8.4, GHC == 7.10.1 synopsis:       Grammar products and higher-dimensional grammars description:+                <http://www.bioinf.uni-leipzig.de/Software/gADP/ generalized Algebraic Dynamic Programming>+                .                 An algebra of liner and context-free grammars.                 .                 This library provides the implementation of our theory of@@ -35,25 +38,9 @@                 pretty-printed in various ways (LaTeX, ANSI, Haskell module                 with signature and grammar).                 .-                .-                .-                Formal background can be found in two papers:-                .-                @-                Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.-                Product Grammars for Alignment and Folding.-                2014. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99.-                <http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6819790>-                @-                .-                and-                .-                @-                Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler-                How to Multiply Dynamic Programming Algorithms-                Brazilian Symposium on Bioinformatics (BSB 2013)-                Lecture Notes in Bioinformatics 8213, Springer, Heidelberg-                @+                The formal background can be found in two papers given in the+                README. The gADP homepage has further details, tutorials,+                examples.                 .  @@ -69,23 +56,20 @@   default:      False   manual:       True -flag llvm-  description:  build using LLVM-  default:      False-  manual:       True  - library   build-depends: base               >= 4.7      && < 4.9+               , ADPfusion          >= 0.4.1    && < 0.4.2                , ansi-wl-pprint     >= 0.6      && < 0.7                , bytestring         >= 0.10     && < 0.11                , containers         >= 0.5      && < 0.6                , data-default       >= 0.5      && < 0.6-               , FormalGrammars     == 0.2.0.*+               , FormalGrammars     >= 0.2.1    && < 0.2.2                , lens               >= 4        && < 5                , newtype            >= 0.2      && < 0.3                , parsers            >= 0.12     && < 0.13+               , PrimitiveArray     >= 0.6.0.1  && < 0.6.2                , semigroups         >= 0.15     && < 0.17                , template-haskell   >= 2        && < 3                , transformers       >= 0.4      && < 0.5@@ -153,13 +137,13 @@ executable AlignGlobal   if flag(examples)     build-depends: base               >= 4.7      && < 4.9-                 , ADPfusion          == 0.4.0.*+                 , ADPfusion                  , containers                  , FormalGrammars                  , GrammarProducts-                 , PrimitiveArray     == 0.6.0.*+                 , PrimitiveArray                  , template-haskell-                 , vector             == 0.10.*+                 , vector             >= 0.10     && < 0.11     buildable: True   else     buildable: False@@ -183,11 +167,6 @@     -funbox-strict-fields     -funfolding-use-threshold1000     -funfolding-keeness-factor1000-  if flag(llvm)-    ghc-options:-      -fllvm-      -optlo-O3-      -fllvm-tbaa
README.md view
@@ -1,17 +1,27 @@-Grammar Products-================+# GrammarProducts: Products of formal languages  [![Build Status](https://travis-ci.org/choener/GrammarProducts.svg?branch=master)](https://travis-ci.org/choener/GrammarProducts) -[*generalized ADPfusion Homepage*](http://www.bioinf.uni-leipzig.de/Software/gADP/)+[*generalized Algebraic Dynamic Programming Homepage*](http://www.bioinf.uni-leipzig.de/Software/gADP/)  An algebra of liner and context-free grammars. +1.  Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.  +    *Product Grammars for Alignment and Folding*  +    2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99  +    [paper](http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6819790)  +1.  Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.  +    *How to Multiply Dynamic Programming Algorithms*  +    2013, Brazilian Symposium on Bioinformatics (BSB 2013)  +    Lecture Notes in Bioinformatics 8213. Springer, Heidelberg.  +    [paper](http://dx.doi.org/10.1007/978-3-319-02624-4_8) [preprint](http://www.bioinf.uni-leipzig.de/Software/gADP/gramprod/hoe-hof-2013.pdf)    + #### Contact -Christian Hoener zu Siederdissen-choener@bioinf.uni-leipzig.de-Leipzig University, Leipzig, Germany+Christian Hoener zu Siederdissen  +Leipzig University, Leipzig, Germany  +choener@bioinf.uni-leipzig.de  +http://www.bioinf.uni-leipzig.de/~choener/
changelog.md view
@@ -1,3 +1,9 @@+0.1.1.0+-------++- FormalGrammar == 0.2.1.x with revamped indexed rules system+- new travis.yml+ 0.1.0.0 -------